Friday, November 06, 2015

The cost of a new gene

Let's think about the biochemical cost associated with adding some new piece of DNA to an existing genome. Michael Lynch has been thinking about this for a long time. He notes that there certainly IS a cost (burden) because the new bit of DNA has to be replicated. That means extra nucleotides have to be synthesized and polymerized every time a cell replicates.

This burden might seem prohibitive for strict adaptationists1 since everything that's detrimental should be lost by negative selection. Lynch, and others, ague that the cost is usually quite small and if it's small enough the detrimental effect might be below the threshold that selection can detect. When this happens, new stretches of DNA become effectively neutral (nearly neutral) and they can be fixed in the genome by random genetic drift.

The key parameter is the size of the population since the power of selection increases as the population size increases. Populations with large numbers of individuals (e.g. more than one million) can respond to the small costs/burdens and eliminate excess DNA whereas populations with smaller numbers of individuals cannot.

Michael Lynch and Georgi Marinov (Hi, Georgi!) have just published a paper where they attempt to calculate the cost of adding DNA as well as the cost associated with transcribing that DNA and translating it into protein (Lynch and Marinov, 2015). One of the goals of the paper is to figure out the overall selective advantage of a new gene given that its product might confer selective advantage when there's an energy cost—in ATP equivalents—associated with every new gene.

Here's how they put it ...

Based on its phenotypic manifestations, a gene may have a multiplicity of advantages, but the energetic cost of replication, maintenance, and expression represents a minimum burden that must be overcome to achieve a net selective advantage. If a genic variant or a novel gene is to be efficiently promoted by natural selection, the net selective advantage (beyond the energetic cost) must exceed the power of drift (defined as 1/Ne for a haploid organism, where Ne is the effective population size).

This is all standard stuff. The innovative parts of the paper are: (1) more specific calculations of costs based on experimental results in the literature, and (2) whether the cost of a gene is related to cell size.

Why is this second goal significant? Because extreme complexity and multicellularity are only seen in eukaryotic cells and eukaryotic cells are much larger than prokaryotic cells. Larger cells require much more protein (and membranes) than small cells so each eukaryotic gene has to produce a lot more proteins than a the same gene in a small cell. The cost of adding a gene to the genome is small compared to the cost of making proteins. Cells could not grow larger and more complex as long as they were limited in their energy production.

Nick Lane and Bill Martin (Lane and Martin, 2010) have argued that eukaryotic cells overcame this limitation due to the inclusion of mitochondria. This allows the cell to produce much more energy making the cost of a gene (mostly protein synthesis) less detrimental than it would be if cell size and complexity increased in prokaryotic cells.

Lynch and Marinov looked at the cost of replicating DNA, the cost of making mRNA, and the cost of making proteins in different cells. The results show that increased cell size does not impose a significantly increased energy burden so there's no need to speculate that mitochondria were necessary for expanded genomes and more complexity. Population genetics can account for the observations.

Taken together, our observations suggest that an energetic boost associated with the emergence of the mitochondrion was not a precondition for eukaryotic genome expansion.

This is probably a bit too much for most of you so I'll concentrate on the other conclusions. These are things you have to know if you want to understand genome evolution.

Bacterial species (prokaryotes) typically have large population sizes. The cost/burden of adding even small amounts of DNA to the genome in these cells is sufficiently detrimental that it can be detected by natural selection. This is why bacterial genomes tend to be small and compact.

The preceding results indicate that the energetic cost of replicating a DNA segment of even just a few nucleotides (even if nontranscribed) can be sufficient to be perceived by selection in a typical bacterial population with large Ne.

Eukaryotic species, especially multicellular eukaryotic species, tend to have small population sizes. In this case, the detrimental cost of adding extra DNA cannot be detected by natural selection so there's no impediment to expanding the genome.

In contrast, insertions of even many kilobases often impose a small enough energetic burden relative to the overall requirements of eukaryotic cells to be immune to selection.

Transcription is also expensive so when a new segment of DNA is transcribed as well as replicated it imposes an even greater cost. However, the extra burden of transcription is still not sufficient to make the cost subject to natural selection in eukaryotic species. Junk RNA is not that harmful. Pervasive transcription is not that harmful.

Although RNA-level costs are frequently greater than those at the DNA level, these are often still not large enough to overcome the power of random genetic drift in eukaryotic cells. This means that many nonfunctional DNAs that are inadvertently, even if specifically, transcribed in eukaryotes (especially in multicellular species) cannot be opposed by selection, a consideration relevant to the debate as to whether transcriptional activity is an indicator of functional significance.

Protein synthesis is expensive. If a new gene has to produce a lot of protein then the cost/burden can be prohibitive, even in eukaryotic species with small populations. This cost has to be overcome by a greater selective advantage to making the proteins. This is why a multicellular eukaryote can have lots of junk DNA making lots of junk RNA but NOT lots of junk protein. It's also why most accidental protein-coding gene duplications usually result in selection for turning off one of the copies.

However, with the cost at the protein level generally being much greater than that at the RNA level, segments of DNA that are translated can sometimes impose a large enough energetic cost to be susceptible to selection, even in multicellular species. This may explain why redundant duplicate genes commonly experience high rates of nonfunctionalization.

1. And for Intelligent Design Creationists who think that strict adapationism (Darwinism) is the only scientific game in town.

40 comments
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In eukaryotes the probable main evolutionary cost of a new gene (assuming it really is a new piece of DNA in the genome) is that since the new gene will initially occur on only one of the parental homologs it will be a small region of haploidy in an otherwise diploid genome potentially causing pairing problems in meiosis thereby decreasing fertility.

Not a bad point that the costs early on would include factors other than the cost of additional nucleotides, etc. But I think from what we know about pairing between homologs that the small duplicated region will most likely just be 'ignored' while the homologs just pair & recombine around it. That is, it would work its way through that challenging time with infrequent problems. The loss of fertility would be small (especially for males), but this cost can be added into the equation.

When we're talking about eukaryotic multicellular vs bacterial/single-cellular population sizes, what are the ranges looked at here? Though large multicellular eukaryote population sizes never reach the scales of bacteria, it still seems to me there are many species with population sizes in the millions. Particularly for plants. Yet many plant genomes are colossal.

How about Jellyfish? They have ridiculous population sizes, how big are their genomes? Is energy abundant for them?

Ridiculous population size for a metazoan, but still very small compared to bacteria. And of course, population size and effective population size can differ quite a bit.

Also, if you look at the figure, the top scale show 1/s (where s is the selection coefficient), and the vertical dotted lines the likely range of N_e. For C. elegans that's in the 10^6 neighborhood, as it is for many invertebrates. So millions indeed.

But N_e it's on the order of 10^9 and up to one or two logs above that for bacteria. But it cannot get many orders of magnitude larger because population size is not the same as effective population size. Even though there are bacteria estimated to have absolute population sizes 10^20 and larger...

A similar calculation would show the same thing for insertion of a small piece of junk DNA (say, 4000 bases). We know processes, such as transposition, can do that. There might be some selective advantage to adding or deleting such a piece, but the power of selection in such a case would be inadequate to explain why the piece of junk DNA is inserted there, or that it is actively maintained there.

A power calculation analogous to Lynch and Marinov's would be needed before credence could be given to any assertion that junk DNA is present because it has a protective effect or because it is needed as spacer.

Polymerization reduces the cost of active transport (where applicable) by lowering intracellular concentration of monomers. This also needs to be included in the terms of the cost equation, as well as stress response based catabolism. Nice to see some thinking around this!

Dazz, I tried to present some of my observations on genetics of polyploids, but there was a glitch in the reply function and they're further down the thread. Perhaps uninteresting, too, but that's a different issue.

This means that many nonfunctional DNAs that are inadvertently, even if specifically, transcribed in eukaryotes (especially in multicellular species) cannot be opposed by selection, a consideration relevant to the debate as to whether transcriptional activity is an indicator of functional significance.

A subtle hint at ENCODE?

Anyway, this is fascinating stuff, don't have access to the paper but would mostly go well above my head anyway.

Also, my position on these issues should have been clear from my posts for a long time. In any case, my PhD thesis will become public in January (it is still visible only within the Caltech network) so everyone will be able to read what exactly I had to say about these things two years ago.

Thanks Larry. Already read Graur's critique of ENCODE, I remember him pointing out that assuming function when there's transcription is far too loose a criteria for functionality. Off to read the rest of those references.

@Georgi: So is the issue with ENCODE not so much about the data or their methodology, but their interpretation of the data?

I'm dubious about the primacy of population-size arguments across this boundary. There are so many internal and external mechanistic differences between prokaryotes and eukaryotes, and many of them must have some influence, potentially overriding.

Then there is the ecological case. Population size in prokaryotes is slippery anyway, but immediate competition with neighbours is likely to be more significant than a hypothetical LLN effect in a largely imaginary efficiently stirred group of relatives.

When you add in multicellularity, dynamics change again. A prokaryote has little leisure time. Meanwhile a multicellular eukaryote has to replicate the extra bases into every somatic cell - but then, those somatic cells themselves are likely to be a substantial cost. They bring benefits beyond their cost, of course, which is not necessarily the case for a bit of junk. Still, in a population of well-fed eukaryotes, irrespective of its size, the nutritional cost of the bases is likely to be small, and the selective cost of a few extra is measured against conspecifics, not against a species in a different niche.

It's not just a constant s value being evaluated by populations of varying size, but highly variable s values depending on a population's closeness to the limits of adequate nutrition, and circumstantial mechanistic effects of radically different life histories and cellular mechanism.

Excellent points. In my evolution class I teach about the bloating of the eukaryote genome as a kind of 'ratchet' process where there are occasional added elements to the genome by regional duplication, transposons, etc., and that selection is not sufficient to remove these since the cost is too low for natural selection to work on it. But the detail here, that selection will be more effective on protein coding genes since they cost more - that is really cool. It is going into my description of this. Thanks.

But the detail here, that selection will be more effective on protein coding genes since they cost more - that is really cool.

I think it also contributes to explaining the C-value paradox. The total genome size in macroscopic eukaryotes is free to vary by a few orders of magnitude, whereas the protein-coding part and the number of protein-coding genes are roughly constant (or at least not wildly different across taxa).

I once did an isozyme study of cottonwoods, which are considered diploid (with two copies of every gene) but are actually diploidized ancient polyploids. (The study involved basic metabolic genes that virtually all eukaryotes have.) In one species I'd score the results for each protein as having two copies, two copies, two copies -- oops, there were clearly four copies of the next gene. In the next species, there'd be only two copy of that gene, but four of something else.

It takes a long time to get rid of the extra copies, Most tetraploid plants (with four copies of each gene) that I studied had four copies of each one. It seems to me that very high polyploids are less stable. I can't say that from scoring isozyme gels for high polyploids -- impossibly confusing -- but from flow cytometry results. If you consider the amount of DNA per cell to be 1 in a diploid, closely related tetraploids will have 2, but closely related decaploids (with 10 copies of each gene) will have, say, 4.3 times as much DNA, not 5 times. Some has been loss.

There are some restrictions on the DNA loss. Obviously, loosing junk DNA isn't a problem (except for getting chromosomes to line up at meiosis, which is often less of a problem than one might think). But consider the case where protein A interacts with protein B. Loosing the gene for A may leave a lot of protein B floating around the cell. Maybe no problem, but sometimes a problem.

Also, one copy may mutate to produce a somewhat different version of the protein. Sometimes that second version does a different useful job or simply does the same job under different conditions. In nearly all cases I worked on where the plant was tetraploid and a gene had three or more alleles (variants), that gene could be scored as one copy of the gene being invariant, and the second copy have two or more or more variations. Perhaps I'm being unclear; it could be scored as having all the variation confined to just one copy of the gene. I have interpreted this as meaning that one copy of the gene had to be just right. The other copy was free to vary, even fail.

In nearly all cases I worked on where the plant was tetraploid and a gene had three or more alleles (variants), that gene could be scored as one copy of the gene being invariant, and the second copy have two or more or more variations. Perhaps I'm being unclear; it could be scored as having all the variation confined to just one copy of the gene. I have interpreted this as meaning that one copy of the gene had to be just right. The other copy was free to vary, even fail.

Do you mean that, in a polyploid, as long as one gene keeps it's original function, it doesn't matter is a copy of the gene suffers a deleterious mutation, the organism is (or can be) still viable?

That would confer polyploids a great selective advantage and explain why they're not selected out, if I got this right?

Yes, I think that that's often the case. Often, polyploidy allows a population to "explore" the consequences of many mutations as long as (at least) one copy of the critical genes retains its original function.

There are some advantages of polyploidy itself. With more copies of each gene, the necessary amount of protein can be made faster. Therefore, polyploidy is very common in plants of cold arctic and alpine habitats, where chemical reactions are slower and the growing season is short.

Also, polyploid cells are usually larger than diploid cells. If the polyploid and diploid plants are the same size, polyploids have fewer cells. And sometimes polyploids are bigger or have thicker leaves, etc.

However, I think by the far most interesting difference is that polyploidization frees up genes to change in potentially important ways.

If any of the pros feels like recommending some good read that's appreciated :)

One thing (or two) that is not clear to me is, if in a diploid there's a recessive and a dominant allele, the dominant rules, but what happens in a tetraploid with 3 recessive alleles vs 1 dominant? I take it from what you said that polyploids can make proteins faster that 2 copies of the gene would be active in a tetraploid, right?

Dominant - Recessive -> DominantRecessive - Recessive -> Recessive

So I guess in this example there would be a dominant and a recessive allele both active. How can that be?

Dominant and recessive are the ideas to start with, but the reality is more complicated. In many cases, recessive genes are "broken." They either don't make a protein at all, or the protein doesn't work property.

But consider hair color in cattle. Black is dominant to red, but shorthorn white is co-dominant to black and to red. An animal with the black and shorthorn white alleles has a mix of black and white hairs, and looks grayish. It's called a blue roan.

In the tetraploids I worked with, nearly all the alleles were expressed -- all made functional proteins.

In a few cases, one of the alleles was a "null." It didn't make a protein that worked, or at least worked under the testing conditions. It was recessive.

I see. So connecting those ideas above, a tetraploid could potentially have four expressed copies of a gene, three of which can be (deleterious) "mutants" and still don't hinder the unmodified copy (enough to be selected out) to perform it's original function? That's really cool stuff

I know it's common to talk about massive bacterial population sizes, but this is a gross oversimplification. Yes some populations of bacterial species in nature are massive, but many bacterial species live in relatively small numbers (on the order of multicellular organisms), see any microbiome paper for examples.So my question is, based on the power of drift, do these bacteria found in small population sizes have more variation in their genome size?

Can you give examples of free-living bacteria with very low effective population size? I am not aware of any (which, of course, does not mean there aren't).

In any case, the theory is not that if N_e is low then the genome will grow big. The theory is that if N_e is low, then the genome is shaped to a greater extent by mutational processes and to a lesser extent by selection than it would be if N_e was large. Then what exactly happens depends on the direction of those mutational processes.

Reading the DNA-seq papers identify many 'new' bacteria in various environments that, at least by high throughput sequencing, appear to be in low abundance. Will have to dig through some papers to find specific examples. Will be a couple of days though as my lab is moving tomorrow and that's a whole lot of fun.

Fair enough, but I expect there are populations of bacterial species that do not are similar in size to multicellular organisms. I also understand that a low N_e does not necessitate an increased genome size, but based on the argument used in the post it seems to link the two. Regardless, I would not be surprised if some bacterial species have larger genome sizes at least until the point where the energy of replication starts to make a difference. Not all bacteria are rapidly growing E. coli-like organisms.

Laurence A. Moran

Larry Moran is a Professor in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

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My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.